Python 2/3 compatibility in single code base, plus python 3 testing on travis.

.travis.yml

-language: cpp
-compiler:
-  - clang
+language: python
+python:
+  - "2.7_with_system_site_packages"
+  - "3.4"
+
 sudo: false
 addons:
   apt:
@@ -10,16 +12,10 @@ addons:
       - libpcre3
       - libpcre3-dev
       - gromacs
-      - swig
       - doxygen
-      - clang-3.3
-      - llvm-3.3
       - python-numpy
       - python-scipy
-      - python-sphinx
-      - python-yaml
-      - python-pip
-      - python-virtualenv
+
 
 env:
   matrix:
@@ -29,11 +25,14 @@ env:
 before_install:
   - export CC=clang
   - export CXX=clang++
-  - export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
+
+  - wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2
+  - mkdir $HOME/swig
+  - tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig
+  - export PATH=$HOME/swig/bin:$PATH
+  - export SWIG_LIB=$HOME/swig/share/swig/3.0.2
 
 script:
-  - virtualenv --system-site-packages openmm_env
-  - source openmm_env/bin/activate
   - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM -DOPENMM_BUILD_STATIC_LIB=$OPENMM_BUILD_STATIC_LIB .
   - make -j2
   - make -j2 install
@@ -41,13 +40,14 @@ script:
   - # Run the testInstallation script
   - python -m simtk.testInstallation
   - # run all of the tests, making sure failures at this stage don't cause travis failures
-  - ctest -j2 -V || true
+  - ctest -j2 || true
   - # get a list of all of the failed tests into this stupid ctest format
-  - python -c 'fn = "Testing/Temporary/LastTestsFailed.log"; import os; os.path.exists(fn) or exit(0); l = [line.split(":")[0] for line in open(fn)]; triplets = zip(l, l, [","]*len(l)); print "".join(",".join(t) for t in triplets)' > FailedTests.log
+  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
   - # rerun all of the failed tests
-  - if [ -s FailedTests.log ]; then ctest -V -I FailedTests.log; fi;
+  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then ctest -I FailedTests.log; fi;
   - # run the python tests too
-  - cd python/tests
-  - pip install nose
-  - nosetests -vv --processes=-1 --process-timeout=200
+  - cd python/tests  
+  - # nosetests -vv --processes=-1 --process-timeout=200
+  - # nosetests -vv
+  - py.test -v *
   - cd -

CMakeLists.txt

 #---------------------------------------------------
-# OpenMM 
+# OpenMM
 #
 # Creates OpenMM library.
 #
@@ -43,11 +43,11 @@ SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake_modules")
 # (cmake 2.4.7 is OK)
 if(COMMAND cmake_policy)
     if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
-        cmake_policy(SET CMP0003 NEW) 
-        cmake_policy(SET CMP0005 NEW) 
+        cmake_policy(SET CMP0003 NEW)
+        cmake_policy(SET CMP0005 NEW)
     endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
     if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
-        cmake_policy(SET CMP0011 NEW) 
+        cmake_policy(SET CMP0011 NEW)
     endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
 endif(COMMAND cmake_policy)
 
@@ -70,7 +70,7 @@ ENDIF (ANDROID)
 # It seems that on linux and mac, everything is trying to be installed in /usr/local/openmm
 # But if every install target is prefixed with /openmm/, on Windows the install files
 # end up in C:/Program Files/OpenMM/openmm/ which is ugly.
-# Better to set CMAKE_INSTALL_PREFIX to /usr/local/openmm and leave /openmm/ off the 
+# Better to set CMAKE_INSTALL_PREFIX to /usr/local/openmm and leave /openmm/ off the
 # install target names.  Plus, the user now has the opportunity to install into /usr/local/
 # if she so chooses.  --cmb
 IF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
@@ -121,6 +121,12 @@ IF (APPLE AND (NOT PNACL))
 ELSE (APPLE AND (NOT PNACL))
     IF (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS)
+        IF (MSVC)
+            # Use warning level 2, not whatever warning level CMake picked.
+            STRING(REGEX REPLACE "/W[0-4]" "/W2" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+            # Explicitly suppress warnings 4305 and 4244.
+            SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4305 /wd4244")
+        ENDIF (MSVC)
     ELSE (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS "-msse2")
     ENDIF (MSVC OR ANDROID OR PNACL)
@@ -139,7 +145,7 @@ IF (NOT CMAKE_CXX_FLAGS_RELEASE)
         SET(CMAKE_CXX_FLAGS_RELEASE "-mfloat-abi=softfp -march=armv7-a -mfpu=neon -funsafe-math-optimizations -O3 -DNDEBUG" CACHE STRING
         "To use when CMAKE_BUILD_TYPE=Release" FORCE)
     ELSE (ANDROID)
-        SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING 
+        SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING
         "To use when CMAKE_BUILD_TYPE=Release" FORCE)
     ENDIF (ANDROID)
 ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
@@ -202,11 +208,11 @@ SET(STATIC_TARGET ${OPENMM_LIBRARY_NAME}_static)
 ## If no one says otherwise, change the executable path to drop into the same binary
 ## location as the DLLs so that the test cases will use the just-build DLLs.
 IF(NOT EXECUTABLE_OUTPUT_PATH)
-  SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR} 
+  SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}
       CACHE INTERNAL "Single output directory for building all executables.")
 ENDIF(NOT EXECUTABLE_OUTPUT_PATH)
 IF(NOT LIBRARY_OUTPUT_PATH)
-  SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR} 
+  SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}
       CACHE INTERNAL "Single output directory for building all libraries.")
 ENDIF(NOT LIBRARY_OUTPUT_PATH)
 SET(${PROJECT_NAME}_EXECUTABLE_DIR ${EXECUTABLE_OUTPUT_PATH}/${CMAKE_CFG_INTDIR})
@@ -221,7 +227,7 @@ SET(API_INCLUDE_DIRS) # start empty
 FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
     # append
     SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
-                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include 
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
                          ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/openmm
                          ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/openmm/internal)
 ENDFOREACH(subdir)
@@ -287,6 +293,9 @@ IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
         SET(EXTRA_LINK_FLAGS "${EXTRA_LINK_FLAGS} -Wl,--no-as-needed -lrt")
     ENDIF (NOT ANDROID)
 ENDIF (CMAKE_SYSTEM_NAME MATCHES "Linux")
+IF (MSVC)
+    SET(EXTRA_LINK_FLAGS)
+ENDIF (MSVC)
 
 IF(OPENMM_BUILD_SHARED_LIB)
     ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
@@ -358,7 +367,7 @@ IF(CUDA_FOUND)
     SET(OPENMM_BUILD_CUDA_LIB ON CACHE BOOL "Build OpenMMCuda library for Nvidia GPUs")
 
     # I wish I was not hardcoding /MD here
-    # Avoid strange windows link error with cuda free energy 
+    # Avoid strange windows link error with cuda free energy
     # plugin by specifying /MD to CUDA_NVCC_FLAGS
     MARK_AS_ADVANCED(CLEAR CUDA_NVCC_FLAGS)
     IF(MSVC)
@@ -374,7 +383,7 @@ IF(CUDA_FOUND)
             if(CUDA_NVCC_FLAGS)
                 set(new_flags "${CUDA_NVCC_FLAGS};${new_flags}")
             endif(CUDA_NVCC_FLAGS)
-            SET(CUDA_NVCC_FLAGS "${new_flags}" 
+            SET(CUDA_NVCC_FLAGS "${new_flags}"
                 CACHE STRING "Semicolon delimit multiple arguments" FORCE)
         ENDIF(NOT HAS_NVCC_FLAG)
     ENDIF(MSVC)

appveyor.yml

+os: Windows Server 2012 R2
+shallow_clone: true
+install:
+
+# Setup shell for VS2010, x64, release mode
+  - >
+    "%ProgramFiles%\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 /release
+
+# Set path to python, git-bash tools.
+  - "set PATH=C:\\Python34-x64;C:\\Python34-x64\\Scripts;%PATH%"
+  - "set PATH=C:\\Program Files (x86)\\Git\\bin;%PATH%"
+  - pip install nose
+
+# Download FFTW3 for PME plugin
+  - C:\MinGW\msys\1.0\bin\wget -q ftp://ftp.fftw.org/pub/fftw/fftw-3.3.4-dll64.zip
+  - 7z x fftw-3.3.4-dll64.zip -oC:\fftw > null
+  - cd C:\fftw
+  - lib /def:libfftw3f-3.def
+  - cd %APPVEYOR_BUILD_FOLDER%
+  - "set PATH=C:\\fftw;%PATH%"
+
+# Download and install some OpenMM build dependencies (doxygen, swig)
+  - choco install -y doxygen.portable swig jom
+
+# Set CMake options
+  - ps: $env:CMAKE_FLAGS='-DOPENMM_BUILD_PME_PLUGIN=ON -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib -DFFTW_INCLUDES=C:/fftw -DCMAKE_BUILD_TYPE=Release -DOPENMM_BUILD_EXAMPLES=OFF -DCMAKE_CXX_FLAGS_RELEASE="/MD /Od /Ob0 /D NDEBUG"'
+  - mkdir build
+  - cd build
+  - cmake -G "NMake Makefiles JOM" %CMAKE_FLAGS% -LA ..
+
+# Run the build
+  - cmake --build . --target install
+  - cmake --build . --target PythonInstall
+
+build: false
+test_script:
+  - ctest || exit 0
+  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
+  - ps: >
+     If (Test-Path "Testing\\Temporary\\LastTestsFailed.log") {
+         cat Testing\\Temporary\\LastTestsFailed.log
+         cat FailedTests.log
+         ctest -I FailedTests.log
+     }
+  - cd python\tests
+  - nosetests -vv --processes=-1 --process-timeout=200
+  - cd %APPVEYOR_BUILD_FOLDER%

docs-source/developerguide/conf.py

@@ -142,7 +142,7 @@ html_static_path = ['_static']
 #html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+html_use_index = False
 
 # If true, the index is split into individual pages for each letter.
 #html_split_index = False

docs-source/usersguide/conf.py

@@ -142,7 +142,7 @@ html_static_path = ['_static']
 #html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+html_use_index = False
 
 # If true, the index is split into individual pages for each letter.
 #html_split_index = False

examples/CMakeLists.txt

@@ -28,7 +28,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
         SET_TARGET_PROPERTIES(${EX_ROOT}
             PROPERTIES
             PROJECT_LABEL "Example - ${EX_ROOT}"
-            LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
             COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
         TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
     ENDIF (OPENMM_BUILD_SHARED_LIB)
@@ -40,7 +40,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
         SET_TARGET_PROPERTIES(${EX_STATIC}
             PROPERTIES
             PROJECT_LABEL "Example - ${EX_STATIC}"
-            LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
             COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
         TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
     ENDIF (OPENMM_BUILD_STATIC_LIB)
@@ -62,7 +62,7 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
             SET_TARGET_PROPERTIES(${EX_ROOT}
                 PROPERTIES
                 PROJECT_LABEL "Example C - ${EX_ROOT}"
-                LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
                 COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
             TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
             ADD_DEPENDENCIES(${EX_ROOT} ApiWrappers)
@@ -77,7 +77,7 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
             SET_TARGET_PROPERTIES(${EX_STATIC}
                 PROPERTIES
                 PROJECT_LABEL "Example C - ${EX_STATIC}"
-                LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
                 COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
             TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
             ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)

olla/src/Kernel.cpp

@@ -38,6 +38,8 @@ Kernel::Kernel() : impl(0) {
 }
 
 Kernel::Kernel(KernelImpl* impl) : impl(impl) {
+    if (impl)
+        impl->referenceCount++;
 }
 
 Kernel::Kernel(const Kernel& copy) : impl(copy.impl) {

olla/src/KernelImpl.cpp

@@ -34,7 +34,7 @@
 using namespace OpenMM;
 using namespace std;
 
-KernelImpl::KernelImpl(string name, const Platform& platform) : name(name), platform(&platform), referenceCount(1) {
+KernelImpl::KernelImpl(string name, const Platform& platform) : name(name), platform(&platform), referenceCount(0) {
 }
 
 std::string KernelImpl::getName() const {

platforms/cpu/sharedTarget/CMakeLists.txt

@@ -18,6 +18,6 @@ ENDFOREACH(file)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/cpu/staticTarget/CMakeLists.txt

@@ -17,6 +17,6 @@ ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 
 TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB_STATIC})
 #-DPTW32_STATIC_LIB only works for the windows pthreads.
-SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
+SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})

platforms/cpu/tests/CMakeLists.txt

@@ -23,7 +23,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ELSE (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
     ENDIF (OPENMM_BUILD_SHARED_LIB)
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

platforms/cuda/include/CudaNonbondedUtilities.h

@@ -142,8 +142,10 @@ public:
     void computeInteractions(int forceGroups);
     /**
      * Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
+     *
+     * @return true if the neighbor list needed to be enlarged.
      */
-    void updateNeighborListSize();
+    bool updateNeighborListSize();
     /**
      * Get the array containing the center of each atom block.
      */

platforms/cuda/sharedTarget/CMakeLists.txt

@@ -18,7 +18,7 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
     SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/cuda/src/CudaIntegrationUtilities.cpp

@@ -201,15 +201,17 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
                 params.push_back(make_float2(dist13, dist12));
             }
             else
-                throw OpenMMException("Two of the three distances constrained with SETTLE must be the same.");
+                continue; // We can't handle this with SETTLE
             isShakeAtom[atom1] = true;
             isShakeAtom[atom2] = true;
             isShakeAtom[atom3] = true;
         }
-        settleAtoms = CudaArray::create<int4>(context, atoms.size(), "settleAtoms");
-        settleParams = CudaArray::create<float2>(context, params.size(), "settleParams");
-        settleAtoms->upload(atoms);
-        settleParams->upload(params);
+        if (atoms.size() > 0) {
+            settleAtoms = CudaArray::create<int4>(context, atoms.size(), "settleAtoms");
+            settleParams = CudaArray::create<float2>(context, params.size(), "settleParams");
+            settleAtoms->upload(atoms);
+            settleParams->upload(params);
+        }
     }
 
     // Find clusters consisting of a central atom with up to three peripheral atoms.

platforms/cuda/src/CudaNonbondedUtilities.cpp

@@ -375,11 +375,16 @@ void CudaNonbondedUtilities::prepareInteractions(int forceGroups) {
 
     if (lastCutoff != kernels.cutoffDistance)
         forceRebuildNeighborList = true;
-    context.executeKernel(kernels.findBlockBoundsKernel, &findBlockBoundsArgs[0], context.getNumAtoms());
-    blockSorter->sort(*sortedBlocks);
-    context.executeKernel(kernels.sortBoxDataKernel, &sortBoxDataArgs[0], context.getNumAtoms());
-    context.executeKernel(kernels.findInteractingBlocksKernel, &findInteractingBlocksArgs[0], context.getNumAtoms(), 256);
-    forceRebuildNeighborList = false;
+    bool rebuild = false;
+    do {
+        context.executeKernel(kernels.findBlockBoundsKernel, &findBlockBoundsArgs[0], context.getNumAtoms());
+        blockSorter->sort(*sortedBlocks);
+        context.executeKernel(kernels.sortBoxDataKernel, &sortBoxDataArgs[0], context.getNumAtoms());
+        context.executeKernel(kernels.findInteractingBlocksKernel, &findInteractingBlocksArgs[0], context.getNumAtoms(), 256);
+        forceRebuildNeighborList = false;
+        if (context.getComputeForceCount() == 1)
+            rebuild = updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
+    } while(rebuild);
     lastCutoff = kernels.cutoffDistance;
 }
 
@@ -389,18 +394,16 @@ void CudaNonbondedUtilities::computeInteractions(int forceGroups) {
     KernelSet& kernels = groupKernels[forceGroups];
     if (kernels.hasForces) {
         context.executeKernel(kernels.forceKernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
-        if (context.getComputeForceCount() == 1)
-            updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
     }
 }
 
-void CudaNonbondedUtilities::updateNeighborListSize() {
+bool CudaNonbondedUtilities::updateNeighborListSize() {
     if (!useCutoff)
-        return;
+        return false;
     unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer();
     interactionCount->download(pinnedInteractionCount);
     if (pinnedInteractionCount[0] <= (unsigned int) maxTiles)
-        return;
+        return false;
 
     // The most recent timestep had too many interactions to fit in the arrays.  Make the arrays bigger to prevent
     // this from happening in the future.
@@ -422,6 +425,7 @@ void CudaNonbondedUtilities::updateNeighborListSize() {
         forceArgs[17] = &interactingAtoms->getDevicePointer();
     findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer();
     forceRebuildNeighborList = true;
+    return true;
 }
 
 void CudaNonbondedUtilities::setUsePadding(bool padding) {

platforms/cuda/staticTarget/CMakeLists.txt

@@ -19,7 +19,7 @@ SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
     SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})

platforms/cuda/tests/CMakeLists.txt

@@ -28,7 +28,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     IF (APPLE)
         SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ELSE (APPLE)
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ENDIF (APPLE)
 
     ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)

platforms/opencl/include/OpenCLNonbondedUtilities.h

@@ -154,8 +154,10 @@ public:
     void computeInteractions(int forceGroups);
     /**
      * Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
+     *
+     * @return true if the neighbor list needed to be enlarged.
      */
-    void updateNeighborListSize();
+    bool updateNeighborListSize();
     /**
      * Get the array containing the center of each atom block.
      */

platforms/opencl/sharedTarget/CMakeLists.txt

@@ -14,6 +14,6 @@ SET_SOURCE_FILES_PROPERTIES(${CL_KERNELS_CPP} ${CL_KERNELS_H} PROPERTIES GENERAT
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/opencl/src/OpenCLContext.cpp

@@ -130,7 +130,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
                             // This will be less than the wavefront width since it takes several
                             // cycles to execute the full wavefront.
                             // The SIMD instruction width is the VLIW instruction width (or 1 for scalar),
-                            // this is the number of ALUs that can be executing per instruction per thread. 
+                            // this is the number of ALUs that can be executing per instruction per thread.
                             devices[i].getInfo<CL_DEVICE_SIMD_PER_COMPUTE_UNIT_AMD>() *
                             devices[i].getInfo<CL_DEVICE_SIMD_WIDTH_AMD>() *
                             devices[i].getInfo<CL_DEVICE_SIMD_INSTRUCTION_WIDTH_AMD>();
@@ -342,9 +342,9 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
         compilationDefines["EXP"] = "exp";
         compilationDefines["LOG"] = "log";
     }
-    
+
     // Set defines for applying periodic boundary conditions.
-    
+
     Vec3 boxVectors[3];
     system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
     boxIsTriclinic = (boxVectors[0][1] != 0.0 || boxVectors[0][2] != 0.0 ||
@@ -392,11 +392,11 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
     }
 
     // Create the work thread used for parallelization when running on multiple devices.
-    
+
     thread = new WorkThread();
-    
+
     // Create utilities objects.
-    
+
     bonded = new OpenCLBondedUtilities(*this);
     nonbonded = new OpenCLNonbondedUtilities(*this);
     integration = new OpenCLIntegrationUtilities(*this, system);
@@ -512,7 +512,7 @@ string OpenCLContext::replaceStrings(const string& input, const std::map<std::st
             if (index != result.npos) {
                 if ((index == 0 || symbolChars.find(result[index-1]) == symbolChars.end()) && (index == result.size()-size || symbolChars.find(result[index+size]) == symbolChars.end())) {
                     // We have found a complete symbol, not part of a longer symbol.
-                    
+
                     result.replace(index, size, iter->second);
                     index += iter->second.size();
                 }
@@ -797,7 +797,7 @@ private:
 
 void OpenCLContext::findMoleculeGroups() {
     // The first time this is called, we need to identify all the molecules in the system.
-    
+
     if (moleculeGroups.size() == 0) {
         // Add a ForceInfo that makes sure reordering doesn't break virtual sites.
 
@@ -879,7 +879,7 @@ void OpenCLContext::findMoleculeGroups() {
                     if (!forces[k]->areParticlesIdentical(mol.atoms[i], mol2.atoms[i]))
                         identical = false;
             }
-            
+
             // See if the constraints are identical.
 
             for (int i = 0; i < (int) mol.constraints.size() && identical; i++) {
@@ -960,11 +960,11 @@ void OpenCLContext::invalidateMolecules() {
     }
     if (valid)
         return;
-    
+
     // The list of which molecules are identical is no longer valid.  We need to restore the
     // atoms to their original order, rebuild the list of identical molecules, and sort them
     // again.
-    
+
     vector<mm_int4> newCellOffsets(numAtoms);
     if (useDoublePrecision) {
         vector<mm_double4> oldPosq(paddedNumAtoms);